Gene loci information

Transcript annotation

  • This transcript has been annotated as Proteasome subunit alpha type-4.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g4076 g4076.t7 TSS g4076.t7 30464628 30464628
chr_3 g4076 g4076.t7 isoform g4076.t7 30464746 30465729
chr_3 g4076 g4076.t7 exon g4076.t7.exon1 30464746 30464752
chr_3 g4076 g4076.t7 cds g4076.t7.CDS1 30464746 30464752
chr_3 g4076 g4076.t7 exon g4076.t7.exon2 30464914 30465377
chr_3 g4076 g4076.t7 cds g4076.t7.CDS2 30464914 30465377
chr_3 g4076 g4076.t7 exon g4076.t7.exon3 30465433 30465729
chr_3 g4076 g4076.t7 cds g4076.t7.CDS3 30465433 30465729
chr_3 g4076 g4076.t7 TTS g4076.t7 30465804 30465804

Sequences

>g4076.t7 Gene=g4076 Length=768
ATGGTAAAAGGTCGTTTGTATCAAGTAGAATATGCTATGGAGGCAATTTCGCATGCTGGT
ACTTGCTTAGGAATTTTAGCAAAAGACGGAATTCTGTTGGCAGCTGAACGCCGAAATATT
AATAAACTTCTCGATAATAGCATCTTTGCTGAAAAGATTTACAGATTAAATGAAGATATG
GTCTGCAGCGTTGCTGGAATTACATCTGATGCAAACGTTCTCACAAATGAGTTACGTTTA
ATTGCACAACGATATCAATTACAGTATGATGAGCCAATTCCAGTTGAACAATTGGTTTCA
AGCTTATGTGATCTAAAGCAAGCATACACACAATATGGTGGTAAACGTCCGTTTGGAGTA
TCGATTCTTTACATGGGTTGGGATAAGCACTATGGATATCAATTGTATCAATCAGATCCA
AGTGGAAATTATAGTGGATGGAAAGCAACATGCATTGGAAATAACGCTGCTGCTGCAATT
TCCGTGCTCAAGCAAGAATTAAATGAAACTCCGATTTCGCTTGCAGAAGCCGAAGATATG
GCAATTAAAGTTCTCTCAAAAACTCTAGACATGACTAAATTGACATCAGAGAAAATTGAA
ATGTCAACTTTGACGAGAACTGAAGAAGGAGAAACAAAAATCAAGATTCTTTCAAATCCA
GAAGTTGATAAATTGATTGCAAATTATGAAAAGATTCAAGCTGAAGAGGAAGCAGCAAAG
AAAGAAAAACTGGCTCAACAACAAGCACAGCAGCAACAAAAATCTTAA

>g4076.t7 Gene=g4076 Length=255
MVKGRLYQVEYAMEAISHAGTCLGILAKDGILLAAERRNINKLLDNSIFAEKIYRLNEDM
VCSVAGITSDANVLTNELRLIAQRYQLQYDEPIPVEQLVSSLCDLKQAYTQYGGKRPFGV
SILYMGWDKHYGYQLYQSDPSGNYSGWKATCIGNNAAAAISVLKQELNETPISLAEAEDM
AIKVLSKTLDMTKLTSEKIEMSTLTRTEEGETKIKILSNPEVDKLIANYEKIQAEEEAAK
KEKLAQQQAQQQQKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4076.t7 CDD cd03752 proteasome_alpha_type_4 4 204 6.67195E-138
6 g4076.t7 Coils Coil Coil 222 254 -
5 g4076.t7 Gene3D G3DSA:3.60.20.10 Glutamine Phosphoribosylpyrophosphate 2 245 2.2E-81
2 g4076.t7 PANTHER PTHR11599:SF13 PROTEASOME SUBUNIT ALPHA TYPE-4 3 231 6.0E-95
3 g4076.t7 PANTHER PTHR11599 PROTEASOME SUBUNIT ALPHA/BETA 3 231 6.0E-95
1 g4076.t7 Pfam PF00227 Proteasome subunit 17 203 3.5E-57
8 g4076.t7 ProSitePatterns PS00854 Proteasome beta-type subunits signature. 23 70 -
9 g4076.t7 ProSiteProfiles PS51475 Proteasome alpha-type subunit profile. 8 226 81.159
4 g4076.t7 SUPERFAMILY SSF56235 N-terminal nucleophile aminohydrolases (Ntn hydrolases) 3 231 4.68E-68

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0019773 proteasome core complex, alpha-subunit complex CC
GO:0051603 proteolysis involved in cellular protein catabolic process BP
GO:0004298 threonine-type endopeptidase activity MF
GO:0005839 proteasome core complex CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values